On 12/14/12 2:28 PM, James Starlight wrote:
Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
No default Bond types
Its strange to me because chromophore itself consist of only one
uncommon bond (in cyclized ring which could produce only several
additional angles and dihedrals)
By comparison in the case of Swiss atom names the total amount of the
same errors was only 9 (all erors about unknown dihedrals with
theadjacent residues. Although I've added capes in that model which
mimicks adjacent residues) it's difficult recognize suitable dihedral
types.
Do you know any others attemps to simulate GFP with chromophore in
charmm with proof parameters ?
This was linked before, at least once:
http://pubs.acs.org/doi/abs/10.1021/jp014476w
The authors provide parameters for everything you need. We used these several
years ago.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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